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- PDB-1lvm: CATALYTICALLY ACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH P... -

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Basic information

Entry
Database: PDB / ID: 1lvm
TitleCATALYTICALLY ACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH PRODUCT
Components
  • (CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)) x 2
  • OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
KeywordsVIRAL PROTEIN / Beta Barrel / Chymotrypsin-type Cystein Protease / Enzyme-peptide Complex
Function / homology
Function and homology information


nuclear-inclusion-a endopeptidase / helper-component proteinase / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / helical viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / symbiont-mediated suppression of host innate immune response ...nuclear-inclusion-a endopeptidase / helper-component proteinase / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / helical viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / symbiont-mediated suppression of host innate immune response / viral translational frameshifting / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding
Similarity search - Function
Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Peptidase family C4 / Potyvirus P1 protease / Potyviridae polyprotein ...Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Peptidase family C4 / Potyvirus P1 protease / Potyviridae polyprotein / Protein P3 of Potyviral polyprotein / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain profile. / Potyviridae P1 protease domain profile. / Potyvirus NIa protease (NIa-pro) domain / Potyvirus NIa protease (NIa-pro) domain profile. / Potyvirus coat protein / Potyvirus coat protein / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Trypsin-like serine proteases / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesTobacco etch virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPhan, J. / Zdanov, A. / Evdokimov, A.G. / Tropea, J.E. / Peters III, H.K. / Kapust, R.B. / Li, M. / Wlodawer, A. / Waugh, D.S.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structural basis for the substrate specificity of tobacco etch virus protease.
Authors: Phan, J. / Zdanov, A. / Evdokimov, A.G. / Tropea, J.E. / Peters III, H.K. / Kapust, R.B. / Li, M. / Wlodawer, A. / Waugh, D.S.
History
DepositionMay 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Remark 999SEQUENCE AUTHOR STATES RESIDUES 308-310 ARE NOT IN THE CRYSTAL OF CHAINS C AND D AND RESIDUES 309- ...SEQUENCE AUTHOR STATES RESIDUES 308-310 ARE NOT IN THE CRYSTAL OF CHAINS C AND D AND RESIDUES 309-310 ARE NOT IN THE PEPTIDE SEQUENCE FOR THIS MUTANT. RESIDUE GLY 308 WAS CLEAVED OFF BY THE ENZYME AND NOT PRESENT IN THE CRYSTAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
E: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)


Theoretical massNumber of molelcules
Total (without water)55,2695
Polymers55,2695
Non-polymers00
Water10,341574
1
A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
E: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)


Theoretical massNumber of molelcules
Total (without water)28,0383
Polymers28,0383
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-15 kcal/mol
Surface area12080 Å2
MethodPISA
2
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE


Theoretical massNumber of molelcules
Total (without water)27,2322
Polymers27,2322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-8 kcal/mol
Surface area10670 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-39 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.505, 75.505, 183.167
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)


Mass: 26147.586 Da / Num. of mol.: 2 / Fragment: Residues 1-221 / Mutation: S219D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tobacco etch virus / Genus: Potyvirus / Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli) / Strain (production host): pRK529 / References: UniProt: P04517
#2: Protein/peptide OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE


Mass: 1084.137 Da / Num. of mol.: 2 / Fragment: Residues 302-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tobacco etch virus / Genus: Potyvirus / Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli) / Strain (production host): pRK529 / References: UniProt: P04517
#3: Protein/peptide CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)


Mass: 805.896 Da / Num. of mol.: 1 / Fragment: Residues 230-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tobacco etch virus / Genus: Potyvirus / Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli) / Strain (production host): pRK529 / References: UniProt: P04517
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulfate, magnesium chloride, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14.5 mg/mlprotein1droppH8.5
20.1 MTris-HCl1reservoir
30.2 M1reservoirMgCl2
410 %glycerol1reservoir
52.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 2001 / Details: Mirrors
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 49988 / Num. obs: 48452 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.058
Reflection shellResolution: 1.8→1.86 Å / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. obs: 49988 / % possible obs: 99.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LVB

1lvb


Resolution: 1.8→25 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 140622.42 / Data cutoff high rms absF: 140622.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 4885 10.1 %RANDOM
Rwork0.171 ---
all-48452 --
obs-48452 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.5232 Å2 / ksol: 0.334191 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20 Å2
2---1.28 Å20 Å2
3---2.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3750 0 0 577 4327
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.31
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it11.753.5
X-RAY DIFFRACTIONc_mcangle_it11.564
X-RAY DIFFRACTIONc_scbond_it16.284
X-RAY DIFFRACTIONc_scangle_it15.914.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 759 10.2 %
Rwork0.243 6658 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. reflection obs: 43567 / Rfactor Rfree: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.31

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